#All sarcomas (ALL)
I applied the dist function to the transpose of the transformed count matrix to get sample-to-sample distances.


There are two groups in the sarcoma PCA which do not cluster according to the sarcoma type, site of disease or HRD score. 
Summary of differentially expressed genes:
##
## out of 20001 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 735, 3.7%
## LFC < 0 (down) : 319, 1.6%
## outliers [1] : 0, 0%
## low counts [2] : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
Summary of differentially expressed genes. Adjusting cut-off for and FDR of 0.05:
##
## out of 20001 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up) : 479, 2.4%
## LFC < 0 (down) : 205, 1%
## outliers [1] : 0, 0%
## low counts [2] : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
Cutoff values: pvalue = 10e-16 FCcutoff = 1.5
Genes upregulated in the treated sample are in the right of the volcano plot, whilst downregulated genes are in the left hand side. 
Summary of differentially expressed genes:
##
## out of 19186 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 28, 0.15%
## LFC < 0 (down) : 9, 0.047%
## outliers [1] : 997, 5.2%
## low counts [2] : 2687, 14%
## (mean count < 19)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
Summary of differentially expressed genes. Adjusting cut-off for and FDR of 0.05:
##
## out of 19186 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up) : 13, 0.068%
## LFC < 0 (down) : 5, 0.026%
## outliers [1] : 997, 5.2%
## low counts [2] : 693, 3.6%
## (mean count < 6)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
Cutoff values: pvalue = 10e-16 FCcutoff = 1.5
Genes upregulated in the HRD high sample are in the right of the volcano plot, whilst downregulated genes are in the left hand side. 
We can observe MAGEC2, MAGEB1, MAGEA3 and PAGE2 upregulated in the HRD high group. However, the number of upregulated genes is very low. ### Counts of most differentially expressed gene


We can observe that MAGEB1, which is one of the most upregulated genes is only up-regulated in three samples. This means that in MFS is difficult to make conclusions based on the RNA seq by comparing HRD high/low groups.

##
## Attaching package: 'shiny'
## The following objects are masked from 'package:DT':
##
## dataTableOutput, renderDataTable
Summary of differentially expressed genes:
##
## out of 19201 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 98, 0.51%
## LFC < 0 (down) : 24, 0.12%
## outliers [1] : 0, 0%
## low counts [2] : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
Summary of differentially expressed genes. Adjusting cut-off for and FDR of 0.05:
##
## out of 19201 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up) : 60, 0.31%
## LFC < 0 (down) : 12, 0.062%
## outliers [1] : 0, 0%
## low counts [2] : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
Cutoff values: pvalue = 10e-16 FCcutoff = 1.5
Genes upregulated in the HRD high sample are in the right of the volcano plot, whilst downregulated genes are in the left hand side. 



Summary of differentially expressed genes:
##
## out of 19549 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 141, 0.72%
## LFC < 0 (down) : 82, 0.42%
## outliers [1] : 0, 0%
## low counts [2] : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
Summary of differentially expressed genes. Adjusting cut-off for and FDR of 0.05:
##
## out of 19549 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up) : 108, 0.55%
## LFC < 0 (down) : 58, 0.3%
## outliers [1] : 0, 0%
## low counts [2] : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
Cutoff values: pvalue = 10e-16 FCcutoff = 1.5
Genes upregulated in the HRD high sample are in the right of the volcano plot, whilst downregulated genes are in the left hand side. 



Summary of differentially expressed genes:
##
## out of 19122 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 586, 3.1%
## LFC < 0 (down) : 171, 0.89%
## outliers [1] : 0, 0%
## low counts [2] : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
Summary of differentially expressed genes. Adjusting cut-off for and FDR of 0.05:
##
## out of 19122 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up) : 369, 1.9%
## LFC < 0 (down) : 74, 0.39%
## outliers [1] : 0, 0%
## low counts [2] : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
Cutoff values: pvalue = 10e-16 FCcutoff = 1.5
Genes upregulated in the HRD high sample are in the right of the volcano plot, whilst downregulated genes are in the left hand side. 
Summary of differentially expressed genes:
##
## out of 19594 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 153, 0.78%
## LFC < 0 (down) : 352, 1.8%
## outliers [1] : 0, 0%
## low counts [2] : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
Summary of differentially expressed genes. Adjusting cut-off for and FDR of 0.05:
##
## out of 19594 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up) : 89, 0.45%
## LFC < 0 (down) : 211, 1.1%
## outliers [1] : 0, 0%
## low counts [2] : 760, 3.9%
## (mean count < 5)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
Cutoff values: pvalue = 10e-16 FCcutoff = 1.5
Genes upregulated in the HRD high sample are in the right of the volcano plot, whilst downregulated genes are in the left hand side. 
Other genes of interest such as B-Catenin (CTNNB1) abd TP53 are also upregulated in the treated group.
Summary of differentially expressed genes:
##
## out of 19356 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 316, 1.6%
## LFC < 0 (down) : 135, 0.7%
## outliers [1] : 858, 4.4%
## low counts [2] : 1074, 5.5%
## (mean count < 11)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
Summary of differentially expressed genes. Adjusting cut-off for and FDR of 0.05:
##
## out of 19356 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up) : 176, 0.91%
## LFC < 0 (down) : 59, 0.3%
## outliers [1] : 858, 4.4%
## low counts [2] : 0, 0%
## (mean count < 4)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
Cutoff values: pvalue = 10e-16 FCcutoff = 1.5
Genes upregulated in the treated sample are in the right of the volcano plot, whilst downregulated genes are in the left hand side. 
Copyright © 2022 Alicia Pliego. FTP lab. All rights reserved.